Like all tactical "real-time" spaceship combat games, I use the pause key (spacebar) a lot, to make it more like a turn-based game. Works very well in this game. I would go nuts (or not even try to master it - it'd be too frustrating for me) if I had to play it without pausing.
In the original SAIS, you could play it in real time with the fixed damage displays without too much trouble. Battles were slower paced, as well, in my estimation.